Plugin for gem that will allow you to uninstall all gems except for those that are 'vaulted'.
$ gem install gem-nuke
$ gem nuke
This will uninstall all gems including gem-nuke itself.
$ gem nuke --vault bundler,gem-nuke,...
This will uninstall all gems except for bundler, gem-nuke and others specified as comma separated gem names.
If you don't want to supply --vault option every time you run gem nuke or just to avoid accidental nuke of important gems,
you can set default value for this option by editing your ~/.gemrc and adding
nuke: --vault gem-nuke,bundler,and_or_other_gems